Package: plier

Version: 1.6.0

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check plier_1.6.0.tar.gz

RetCode: 0

Time: 99.6 seconds

Status: OK

CheckDir: plier.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/bbs-2.0-bioc/meat/plier.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'plier/DESCRIPTION' ... OK
* this is package 'plier' version '1.6.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'plier' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating plier-Ex.R ... OK
* checking examples ... OK
* creating plier-manual.tex ... OK
* checking plier-manual.tex ... OK

* Installing *source* package 'plier' ...
** libs
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c affyplier.cpp -o affyplier.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c plier_impl.cpp -o plier_impl.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:909: warning: 'LogLikelihood' may be used uninitialized in this function
plieralg.cpp: At global scope:
plieralg.cpp:48: warning: 'g_ErrorCode' defined but not used
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp: In function 'void an_experiment(bool*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, bool*, bool*, bool*, double*, double*, int*, int*, int*, int*, double*, double*, char**, double*, double*, int*)':
rwrapper.cpp:341: warning: too many arguments for format
rwrapper.cpp: In function 'void one_probeset(bool*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, bool*, bool*, bool*, double*, double*, int*, int*, int*, long int*, double*, double*, double*, double*, int*)':
rwrapper.cpp:162: warning: 'rpct' is used uninitialized in this function
g++ -G -L/usr/local/lib -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o   -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** help
 >>> Building/Updating help pages for package 'plier'
     Formats: text html latex example 
  justPlier                         text    html    latex   example
** building package indices ...
* DONE (plier)